[gmx-users] Protonation state of phospho-tyrosine in neutral PH

[Justin Lemkul]

On 12/22/16 10:52 AM, Zheng Ruan wrote:
> Hi Gromacs Users,
>
> I'm trying to run simulation on a protein with phosphorylated tyrosine
> residues. The amber force field parameters (http://research.bmh.
> manchester.ac.uk/bryce/amber) provides three different protonation states
> of the phospho-tyrosine residue. What is the predominant form of
> phospho-tyrosine residue in neutral PH? Is there a reference about the PKa
> values associated with each protonation state?
>

https://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/1/p9405pis.pdf

Note that the pKa values of the isolated amino acid may differ slightly from 
those found in a polypeptide chain.  Google searching turns up tons of results 
that are relevant, and you could always just do a pKa calculation with the many 
available tools.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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